Molecular Characterization and Detection of Plasmid-Mediated Quinolone Resistance (qnrA, qnrB, qnrD) Genes among Multidrug-Resistant Salmonella enterica Serovar Typhi Isolates from Clinical Specimens in Bauchi, Northeastern Nigeria

Abstract

Background: Salmonella enterica serovar Typhi remains a leading cause of enteric fever with 9 million cases and 110,000 deaths annually, disproportionately affecting low- and middle-income countries (Lamichhane et al., 2024). Multidrug-resistant (MDR) S. typhi and plasmid-mediated quinolone resistance (PMQR) determinants, particularly qnr genes, pose a major public health threat within the One Health framework because of their potential for rapid horizontal dissemination via mobile genetic elements (Djordjevic et al., 2024; Argimón et al., 2021). Aim: This study aimed to molecularly identify MDR S. typhi isolates and detect qnrA, qnrB and qnrD genes among clinical isolates in Bauchi, Northeastern Nigeria. Place and Duration of Study: Department of Microbiology, Abubakar Tafawa Balewa University, Bauchi, and Abubakar Tafawa Balewa University Teaching Hospital (ATBUTH), Bauchi, Nigeria, between January 2024 and December 2024. Methodology: This was a cross-sectional laboratory-based study. Ethical approval: ATBUTH/HREC/2024/012. A total of 138 clinical samples (blood, n = 66; stool, n = 72) were collected with informed consent. Samples were cultured on Salmonella-Shigella Agar and Xylose Lysine Deoxycholate Agar. Presumptive Salmonella isolates were confirmed biochemically (Triple Sugar Iron, citrate, urease, H2S, motility) and serologically using polyvalent O and H antisera. Antimicrobial susceptibility testing (AST) was performed using the Kirby–Bauer disc diffusion in accordance with CLSI M100, 33rd edition (Clinical and Laboratory Standards Institute, 2023) using 12 antibiotics: ampicillin (10µg), chloramphenicol (30µg), trimethoprim-sulfamethoxazole (25µg), ciprofloxacin (5µg), nalidixic acid (30µg), ceftriaxone (30µg), cefotaxime (30µg), azithromycin (15µg), gentamicin (10µg), tetracycline (30µg), amoxicillin-clavulanate (30µg) and ofloxacin (5µg). MDR was defined as resistance to ≥1 agent in ≥3 antimicrobial categories (Magiorakos et al., 2012). MDR isolates were confirmed by PCR targeting the 16S rRNA gene (RIBOSE-1/RIBOSE-2, 789bp), followed by Sanger sequencing and BLAST analysis (≥98.7% identity threshold) (Stackebrandt and Ebers, 2006; Altschul et al., 1990). PMQR genes (qnrA, 516 bp; qnrB, 469 bp; qnrD, 691 bp) were screened by gene-specific PCR (Robicsek et al., 2006; Cavaco et al., 2009) and phylogenetic analysis was performed in MEGA 11 using the Neighbour-Joining method, 1,000 bootstrap replicates and the Kimura two-parameter model (Kimura, 1980; Tamura et al., 2021). Results: Five (3.62%) Salmonella isolates were recovered (blood: 2/66, 3.03%; stool: 3/72, 4.16%). Two isolates (40%) were multidrug-resistant (MDR) (resistant to ampicillin, chloramphenicol, SXT, nalidixic acid, tetracycline). Sequencing of the 16S rRNA gene showed 99.10% and 98.77% identity with S. typhi reference strains CP156169.1 and CP029896.1. Phylogenetic analysis clustered the isolates with global S. typhi strains. Among MDR isolates, qnrA was detected in 2/2 (100%), qnrB in 1/2 (50%), qnrD 0%. Overall occurrence in the study population: qnrA 2/138 (1.45%), qnrB 1/138 (0.72%). Conclusion: This study confirms the circulation of PMQR determinants (qnrA, qnrB) among MDR S. typhi in Bauchi. Although the prevalence was low (1.45%), their presence in clinical isolates indicates a potential risk of reduced fluoroquinolone effectiveness. Continued molecular surveillance within a One Health framework, antimicrobial stewardship, and WASH interventions are recommended. Future studies should use whole-genome sequencing for plasmid characterization.